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Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
BACKGROUND: A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirement...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326232/ https://www.ncbi.nlm.nih.gov/pubmed/16297241 http://dx.doi.org/10.1186/1471-2105-6-275 |
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author | Jolly, Emmitt R Chin, Chen-Shan Herskowitz, Ira Li, Hao |
author_facet | Jolly, Emmitt R Chin, Chen-Shan Herskowitz, Ira Li, Hao |
author_sort | Jolly, Emmitt R |
collection | PubMed |
description | BACKGROUND: A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. RESULTS: Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. CONCLUSION: We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation. |
format | Text |
id | pubmed-1326232 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-13262322006-01-24 Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis Jolly, Emmitt R Chin, Chen-Shan Herskowitz, Ira Li, Hao BMC Bioinformatics Methodology Article BACKGROUND: A major challenge in computational genomics is the development of methodologies that allow accurate genome-wide prediction of the regulatory targets of a transcription factor. We present a method for target identification that combines experimental characterization of binding requirements with computational genomic analysis. RESULTS: Our method identified potential target genes of the transcription factor Ndt80, a key transcriptional regulator involved in yeast sporulation, using the combined information of binding affinity, positional distribution, and conservation of the binding sites across multiple species. We have also developed a mathematical approach to compute the false positive rate and the total number of targets in the genome based on the multiple selection criteria. CONCLUSION: We have shown that combining biochemical characterization and computational genomic analysis leads to accurate identification of the genome-wide targets of a transcription factor. The method can be extended to other transcription factors and can complement other genomic approaches to transcriptional regulation. BioMed Central 2005-11-18 /pmc/articles/PMC1326232/ /pubmed/16297241 http://dx.doi.org/10.1186/1471-2105-6-275 Text en Copyright © 2005 Jolly et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Jolly, Emmitt R Chin, Chen-Shan Herskowitz, Ira Li, Hao Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
title | Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
title_full | Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
title_fullStr | Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
title_full_unstemmed | Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
title_short | Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
title_sort | genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326232/ https://www.ncbi.nlm.nih.gov/pubmed/16297241 http://dx.doi.org/10.1186/1471-2105-6-275 |
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